From ef9324ca5b7bebdfb4682a16b8a94d9da53adccc Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 30 Jan 2024 10:17:12 +0000 Subject: [PATCH 1/4] Updated tests for the staging monitor classes. Used current staging directories structure. Used run Illumina's native run folder names. Stopped using HiSeq-specific run folder files. --- t/34-monitor-runfolder-staging.t | 277 +++++++++++++++---------------- t/34-monitor-runfolder.t | 108 +++++------- 2 files changed, 180 insertions(+), 205 deletions(-) diff --git a/t/34-monitor-runfolder-staging.t b/t/34-monitor-runfolder-staging.t index b60dab4a..3723727d 100644 --- a/t/34-monitor-runfolder-staging.t +++ b/t/34-monitor-runfolder-staging.t @@ -1,17 +1,16 @@ use strict; use warnings; -use Test::More tests => 50; +use Test::More tests => 9; use Test::Exception; use Test::Warn; use File::Copy; use File::Find; -use File::Temp qw(tempdir); -use File::Path qw(make_path); +use File::Temp qw/tempdir/; +use File::Path qw/make_path/; use Fcntl qw/S_ISGID/; use t::dbic_util; -my $MOCK_STAGING = 't/data/gaii/staging'; my $SECONDS_PER_HOUR = 60 * 60; BEGIN { @@ -23,14 +22,15 @@ BEGIN { my $schema = t::dbic_util->new->test_schema(); sub write_run_params { - my ($id_run, $fs_run_folder, $application_name) = @_; + my ($id_run, $fs_run_folder) = @_; + my $runparamsfile = qq[$fs_run_folder/runParameters.xml]; open(my $fh, '>', $runparamsfile) or die "Could not open file '$runparamsfile' $!"; print $fh <<"ENDXML"; - $application_name + NovaSeq Control Software $id_run @@ -38,20 +38,9 @@ ENDXML close $fh; } -sub write_hiseq_run_params { - my ($id_run, $fs_run_folder) = @_; - my $application_name = q[HiSeq Control Software]; - write_run_params($id_run, $fs_run_folder, $application_name); -} - -sub write_nova_run_params { - my ($id_run, $fs_run_folder) = @_; - my $application_name = q[NovaSeq Control Software]; - write_run_params($id_run, $fs_run_folder, $application_name); -} - sub write_run_files { my ($id_run, $fs_run_folder, $lanes, $cycles) = @_; + $lanes = $lanes || 8; if ( $cycles ) { $cycles = qq[]; @@ -63,7 +52,7 @@ sub write_run_files { ENDXML } - write_hiseq_run_params($id_run, $fs_run_folder); + write_run_params($id_run, $fs_run_folder); my $runinfofile = qq[$fs_run_folder/RunInfo.xml]; open(my $fh, '>', $runinfofile) or die "Could not open file '$runinfofile' $!"; @@ -82,15 +71,23 @@ ENDXML close $fh; } -subtest 'updating run data from filesystem' => sub { - plan tests => 5; +sub touch_file { + my $path = shift; + open(my $fh, '>', $path) or die "Could not touch file '$path' $!"; + close $fh; +} - my $basedir = tempdir( CLEANUP => 1 ); +subtest 'computing glob and updating run data from filesystem' => sub { + plan tests => 7; - my $fs_run_folder = qq[$basedir/IL3/incoming/100622_IL3_01234]; + my $rf_name = q[240124_A00951_0713_AHW3TYDRX3]; + my $staging = tempdir( CLEANUP => 1 ) . + q[/esa-sv-20201215-02/IL_seq_data]; + my $fs_run_folder = $staging . q[/incoming/] . $rf_name; make_path($fs_run_folder); - my $id_run = 1234; + write_run_files($id_run, $fs_run_folder); + my $run_data = { id_run => $id_run, id_instrument => 67, @@ -99,42 +96,39 @@ subtest 'updating run data from filesystem' => sub { expected_cycle_count => 310, actual_cycle_count => 0, }; - - write_run_files($id_run, $fs_run_folder); - my $run = $schema->resultset('Run')->find($id_run); $run->update($run_data); - my $run_folder = Monitor::RunFolder::Staging->new(runfolder_path => $fs_run_folder, - npg_tracking_schema => $schema); + my $run_folder = Monitor::RunFolder::Staging->new( + runfolder_path => $fs_run_folder, + npg_tracking_schema => $schema); isa_ok($run_folder, 'Monitor::RunFolder::Staging'); - - is( $run_folder->_get_folder_path_glob, qq[$basedir/IL3/*/], - 'internal glob correct' ); - lives_ok { $run_folder->update_run_record } 'update folder name and glob in DB'; - is( $run_folder->tracking_run()->folder_name(), '100622_IL3_01234', - ' folder name updated' ); - is( $run_folder->tracking_run()->folder_path_glob(), qq[$basedir/IL3/*/], - ' folder path glob updated' ); + is( $run_folder->tracking_run()->folder_name(), $rf_name, + 'folder name updated' ); + is( $run_folder->tracking_run()->folder_path_glob(), + $staging . q[/*/], 'folder path glob updated'); + + my $glob = '/{export,nfs}/esa-sv-20201215-01/IL_seq_data/*/'; + my $path = '/export/esa-sv-20201215-01/IL_seq_data/outgoing/' . $rf_name; + for my $dir (qw/incoming analysis outgoing/) { + my $rfpath = $path; + $rfpath =~ s/outgoing/$dir/; + note $rfpath; + my $test = Monitor::RunFolder::Staging->new(runfolder_path => $rfpath); + is($test->_get_folder_path_glob, $glob, "glob for /$dir/"); + } }; -sub touch_file { - my ($path) = @_; - - open(my $fh, '>', $path) or die "Could not touch file '$path' $!"; - close $fh; -} - subtest 'folder identifies copy complete for NovaSeq' => sub { plan tests => 12; - my $basedir = tempdir( CLEANUP => 1 ); - - my $fs_run_folder = qq[$basedir/IL3/incoming/100622_IL3_01234]; + my $fs_run_folder = tempdir( CLEANUP => 1 ) . + q[/esa-sv-20201215-02/IL_seq_data/incoming/240124_A00951_0713_AHW3TYDRX3]; make_path($fs_run_folder); - my $id_run = 1234; + write_run_files($id_run, $fs_run_folder); + my $run_data = { id_run => $id_run, id_instrument => 67, @@ -144,32 +138,32 @@ subtest 'folder identifies copy complete for NovaSeq' => sub { actual_cycle_count => 0, # So there is no lag }; - write_run_files($id_run, $fs_run_folder); - write_nova_run_params($id_run, $fs_run_folder); - my $run = $schema->resultset('Run')->find($id_run); $run->update($run_data); - my $run_folder = Monitor::RunFolder::Staging->new(runfolder_path => $fs_run_folder, - npg_tracking_schema => $schema); - + my $run_folder = Monitor::RunFolder::Staging->new( + runfolder_path => $fs_run_folder, + npg_tracking_schema => $schema); ok(!$run_folder->is_run_complete(), 'Run is not complete'); my $path_to_rta_complete = qq[$fs_run_folder/RTAComplete.txt]; my $path_to_copy_complete = qq[$fs_run_folder/CopyComplete.txt]; touch_file($path_to_rta_complete); - ok(!$run_folder->is_run_complete(), 'Only RTAComplete is not enough for NovaSeq'); - - for my $file_name (qw[ CopyComplete Copycomplete copycomplete CopyComplete_old.txt ]) { - note $file_name; - my $path_to_wrong_copy_complete = qq[$fs_run_folder/$file_name]; - touch_file($path_to_wrong_copy_complete); - ok(!$run_folder->is_run_complete(), 'Run is not complete'); - unlink $path_to_wrong_copy_complete or die "Could not delete file $path_to_wrong_copy_complete: $!"; + ok(!$run_folder->is_run_complete(), + 'Only RTAComplete is not enough for NovaSeq'); + + for my $file_name (qw[CopyComplete Copycomplete + copycomplete CopyComplete_old.txt ]) { + note $file_name; + my $path_to_wrong_copy_complete = qq[$fs_run_folder/$file_name]; + touch_file($path_to_wrong_copy_complete); + ok(!$run_folder->is_run_complete(), 'Run is not complete'); + unlink $path_to_wrong_copy_complete or die + "Could not delete file $path_to_wrong_copy_complete: $!"; } - - unlink $path_to_rta_complete or die "Could not delete file $path_to_rta_complete: $!"; + unlink $path_to_rta_complete or die + "Could not delete file $path_to_rta_complete: $!"; touch_file($path_to_copy_complete); my $complete = 1; @@ -179,9 +173,10 @@ subtest 'folder identifies copy complete for NovaSeq' => sub { is($complete, 0, 'Only CopyComplete.txt file is not enough for NovaSeq'); touch_file($path_to_rta_complete); - ok($run_folder->is_run_complete(), 'RTAComplete + CopyComplete is enough for NovaSeq'); - - unlink $path_to_copy_complete or die "Could not delete file '$path_to_copy_complete' $!"; + ok($run_folder->is_run_complete(), + 'RTAComplete + CopyComplete is enough for NovaSeq'); + unlink $path_to_copy_complete or die + "Could not delete file '$path_to_copy_complete' $!"; my ($atime, $mtime) = (stat($path_to_rta_complete))[8,9]; $atime -= 3 * $SECONDS_PER_HOUR; # make it 3 hours ago @@ -189,7 +184,8 @@ subtest 'folder identifies copy complete for NovaSeq' => sub { utime($atime, $mtime, $path_to_rta_complete) or die "couldn't backdate $path_to_rta_complete, $!"; - ok(!$run_folder->is_run_complete(), 'RTAComplete + short wait time is not enough for NovaSeq'); + ok(!$run_folder->is_run_complete(), + 'RTAComplete + short wait time is not enough for NovaSeq'); ($atime, $mtime) = (stat($path_to_rta_complete))[8,9]; $atime -= 9 * $SECONDS_PER_HOUR; # make it 12 hours ago @@ -269,42 +265,42 @@ subtest 'counting cycles and tiles' => sub { is ($test->get_latest_cycle(), 0, 'correct current cycle'); }; -{ +subtest 'moving runfolder' => sub { + plan tests => 32; + + my $tmpdir = tempdir( CLEANUP => 1 ); + my $rf_name = '240125_A01607_0050_AHWF5WDRX3'; + my $test = Monitor::RunFolder::Staging->new( - runfolder_path => $MOCK_STAGING . '/IL3/skip_this_one/090810_IL12_3289', - npg_tracking_schema => $schema); + runfolder_path => $tmpdir . '/IL_seq_data/skip_this_one/' . $rf_name, + npg_tracking_schema => $schema); throws_ok { $test->move_to_analysis() } qr/is\ not\ in\ incoming/msx, - 'Runfolder should be in incoming'; + 'Runfolder should be in incoming'; $test = Monitor::RunFolder::Staging->new( - runfolder_path => $MOCK_STAGING . '/IL3/incoming/incoming/090810_IL12_3289', - npg_tracking_schema => $schema); - throws_ok { $test->move_to_analysis() } qr/contains\ multiple\ upstream\ incoming\ directories/msx, - 'Runfolder path should not contain multiple incoming directories'; + runfolder_path => $tmpdir . '/IL_seq_data/incoming/incoming/' . $rf_name, + npg_tracking_schema => $schema); + throws_ok { $test->move_to_analysis() } + qr/contains\ multiple\ upstream\ incoming\ directories/msx, + 'Runfolder path should not contain multiple incoming directories'; - my $tmpdir = tempdir( CLEANUP => 1 ); $test = Monitor::RunFolder::Staging->new( - runfolder_path => $tmpdir . '/incoming/090810_IL12_3289', - npg_tracking_schema => $schema); - make_path $tmpdir . '/analysis/090810_IL12_3289'; + runfolder_path => $tmpdir . '/incoming/' . $rf_name, + npg_tracking_schema => $schema); + make_path $tmpdir . '/analysis/' . $rf_name; throws_ok { $test->move_to_analysis() } qr/already\ exists/msx, - 'Refuse to overwrite an existing directory'; -} + 'Refuse to overwrite an existing directory'; -{ - my $tmpdir = tempdir( CLEANUP => 1 ); - my $test_source = $tmpdir . '/IL12/incoming/100721_IL12_05222'; - my $analysis_dir = $tmpdir . '/IL12/analysis'; - my $test_target = $analysis_dir . '/100721_IL12_05222'; + $rf_name = '240125_A00708_0693_BH2C2NDSXC'; + my $test_source = $tmpdir . '/IL_seq_data/incoming/' . $rf_name; + my $analysis_dir = $tmpdir . '/IL_seq_data/analysis'; + my $test_target = $analysis_dir . '/' . $rf_name; make_path $test_source; - - ok( !-e $analysis_dir, 'analysis dir does not exist - test prerequisite'); $schema->resultset('Run')->find(5222)->update_run_status('qc complete'); - my $test = Monitor::RunFolder::Staging->new( runfolder_path => $test_source, - npg_tracking_schema => $schema, ); - isnt( $test->tracking_run->current_run_status_description(), 'analysis pending', - 'run status is not analysis pending'); + $test = Monitor::RunFolder::Staging->new(runfolder_path => $test_source, + id_run => 5222, + npg_tracking_schema => $schema); ok( !$test->is_in_analysis(), 'run folder is not in analysis'); my $m; lives_ok { $m = $test->move_to_analysis() } 'Move to analysis'; @@ -314,42 +310,47 @@ subtest 'counting cycles and tiles' => sub { make_path( $analysis_dir ); ok( -e $analysis_dir, 'analysis dir exists - test prerequisite'); lives_ok { $test->move_to_analysis() } - 'No error if analysis directory already exists...'; - + 'No error if analysis directory already exists...'; ok( !-e $test_source, 'runfolder is gone from incoming' ); ok( -e $test_target, 'runfolder is present in analysis' ); - - is( $test->tracking_run()->current_run_status_description(), 'analysis pending', - 'Current run status is \'analysis pending\'' ); + is( $test->tracking_run()->current_run_status_description(), + 'analysis pending', 'Current run status is \'analysis pending\'' ); $test_source = $test_target; - my $outgoing_dir = $tmpdir . '/IL12/outgoing'; - $test_target = $outgoing_dir . '/100721_IL12_05222'; - ok( !-e $test_target, 'outgoing run dir does not exist - test prerequisite'); - $test = Monitor::RunFolder::Staging->new( runfolder_path => $test_source, - npg_tracking_schema => $schema, ); + my $outgoing_dir = $tmpdir . '/IL_seq_data/outgoing'; + $test_target = $outgoing_dir . '/' . $rf_name; + $test = Monitor::RunFolder::Staging->new( runfolder_path => $test_source, + id_run => 5222, + npg_tracking_schema => $schema, ); lives_ok { $m = $test->move_to_outgoing() } 'Move to outgoing lives'; ok( !-e $test_target, 'not in outgoing' ); ok( -e $test_source, 'in analysis' ); - is( $m, 'Run 5222 status analysis pending is not qc complete, not moving to outgoing', - 'not moved since the run status does not fit'); + is($m, 'Run 5222 status analysis pending is not qc complete, ' . + 'not moving to outgoing', + 'not moved since the run status does not fit'); sleep 1; $test->tracking_run()->update_run_status('qc complete'); - $test = Monitor::RunFolder::Staging->new(runfolder_path => $tmpdir . '/IL12/incoming/100721_IL12_05222', - npg_tracking_schema => $schema, ); + $test = Monitor::RunFolder::Staging->new( + runfolder_path => $tmpdir . '/IL_seq_data/incoming/' . $rf_name, + id_run => 5222, + npg_tracking_schema => $schema); throws_ok { $test->move_to_outgoing() } qr/is\ not\ in\ analysis/msx, - 'Runfolder should be in analysis'; + 'Runfolder should be in analysis'; $test = Monitor::RunFolder::Staging->new( - runfolder_path => $tmpdir . '/IL12/analysis/some/analysis/100721_IL12_05222', - npg_tracking_schema => $schema); - throws_ok { $test->move_to_outgoing() } qr/contains\ multiple\ upstream\ analysis\ directories/msx, - 'Runfolder path should not contain multiple upstream analysis directories'; - - $test = Monitor::RunFolder::Staging->new( runfolder_path => $test_source, - npg_tracking_schema => $schema, ); + runfolder_path => $tmpdir . '/IL_seq_data/analysis/some/analysis/' . + $rf_name, + id_run => 5222, + npg_tracking_schema => $schema); + throws_ok { $test->move_to_outgoing() } + qr/contains\ multiple\ upstream\ analysis\ directories/msx, + 'Runfolder path should not contain multiple upstream analysis directories'; + + $test = Monitor::RunFolder::Staging->new(runfolder_path => $test_source, + id_run => 5222, + npg_tracking_schema => $schema); ok( $test->is_in_analysis(), 'run folder is in analysis'); lives_ok { $m = $test->move_to_outgoing() } 'Move to outgoing lives'; ok( !-e $test_target, 'is not in outgoing'); @@ -357,37 +358,36 @@ subtest 'counting cycles and tiles' => sub { ': No such file or directory', 'move is confirmed' ); ok( -e $test_source, 'still in analysis' ); - make_path( $outgoing_dir ); - ok( -e $outgoing_dir, 'outgoing directory exists' ); + make_path $outgoing_dir; lives_ok { $m = $test->move_to_outgoing() } 'Move to outgoing lives'; ok( -e $test_target, 'is in outgoing' ); is( $m, "Moved $test_source to $test_target", 'move is confirmed' ); ok( !-e $test_source, 'gone from analysis' ); throws_ok { $test->move_to_outgoing() } qr/already\ exists/msx, - 'Refuse to overwrite an existing directory'; -} + 'Refuse to overwrite an existing directory'; -{ - my $tmpdir = tempdir( CLEANUP => 1 ); - my $test_source = $tmpdir . '/IL12/incoming/100721_IL12_05222'; - my $analysis_dir = $tmpdir . '/IL12/analysis'; - my $test_target = $analysis_dir . '/100721_IL12_05222'; + $tmpdir = tempdir( CLEANUP => 1 ); + $test_source = $tmpdir . '/IL_seq_data/incoming/' . $rf_name; + $analysis_dir = $tmpdir . '/IL_seq_data/analysis'; + $test_target = $analysis_dir . '/' . $rf_name; make_path $test_source; - make_path( $analysis_dir ); - + make_path $analysis_dir; $schema->resultset('Run')->find(5222)->update_run_status('run pending'); - my $test = Monitor::RunFolder::Staging->new( runfolder_path => $test_source, - status_update => 0, - npg_tracking_schema => $schema, ); + $test = Monitor::RunFolder::Staging->new( runfolder_path => $test_source, + id_run => 5222, + status_update => 0, + npg_tracking_schema => $schema); lives_ok { $test->move_to_analysis() } 'Move to analysis'; ok( !-e $test_source, 'runfolder is gone from incoming' ); ok( -e $test_target, 'runfolder is present in analysis' ); is( $test->tracking_run()->current_run_status_description(), 'run pending', - 'run status is unchanged' ); -} + 'run status is unchanged' ); +}; + +subtest 'monitoring size' => sub { + plan tests => 2; -{ my $tmpdir = tempdir( CLEANUP => 1 ); make_path("$tmpdir/Data/Intensities/Basecalls/L001/C1.1"); copy('t/data/run_info/runInfo.novaseq.xp.lite.xml', "$tmpdir/RunInfo.xml"); @@ -403,16 +403,11 @@ subtest 'counting cycles and tiles' => sub { # Seems a little fragile (and unnecessary) to insist on an exact match. ok( $size > 100, 'Find file size sum' ); -} +}; -{ - my $test = Monitor::RunFolder::Staging->new( runfolder_path => '/nfs/sf25/ILorHSany_sf25/outgoing/110712_HS8_06541_B_B0A6DABXX'); - is($test->_get_folder_path_glob, '/{export,nfs}/sf25/ILorHSany_sf25/*/', 'glob for /nfs/sf25 outgoing'); - $test = Monitor::RunFolder::Staging->new( runfolder_path => '/export/sf25/ILorHSany_sf25/incoming/110712_HS8_06541_B_B0A6DABXX'); - is($test->_get_folder_path_glob, '/{export,nfs}/sf25/ILorHSany_sf25/*/', 'glob for /export/sf25 incoming'); -} +subtest 'seting file system permissions' => sub { + plan tests => 4; -{ my $tmpdir = tempdir( CLEANUP => 1 ); my $r= (stat($tmpdir))[2] & S_ISGID(); ok( !$r, 'initially the gid bit is not set'); @@ -427,7 +422,7 @@ subtest 'counting cycles and tiles' => sub { 'changing group'; $r= (stat($tmpdir))[2] & S_ISGID(); ok( $r, 'now the gid bit is set'); -} +}; subtest 'run completion for NovaSeqX' => sub { plan tests => 5; diff --git a/t/34-monitor-runfolder.t b/t/34-monitor-runfolder.t index a30fef2f..4c1af76c 100644 --- a/t/34-monitor-runfolder.t +++ b/t/34-monitor-runfolder.t @@ -1,8 +1,7 @@ use strict; use warnings; -use English qw(-no_match_vars); use File::Copy; -use Test::More tests => 34; +use Test::More tests => 7; use Test::Exception; use Test::Warn; use File::Temp qw/ tempdir /; @@ -14,71 +13,57 @@ use t::dbic_util; use_ok('Monitor::RunFolder'); my $schema = t::dbic_util->new->test_schema(); -my $MOCK_STAGING = 't/data/gaii/staging'; my $dir4rf = tempdir( CLEANUP => 1 ); -{ - my $mock_path = $MOCK_STAGING . '/IL12/incoming/100721_IL12_05222'; - my $test; - lives_ok { - $test = Monitor::RunFolder->new( runfolder_path => $mock_path, - npg_tracking_schema => $schema, ) - } 'Object creation ok'; - isa_ok( $test, 'Monitor::RunFolder'); - - is( $test->run_folder(), '100721_IL12_05222', - 'Run folder attribute correct' ); +subtest 'test methods for cycle and status update' => sub { + plan tests => 15; + my $rf_name = q[240124_MS8_05222_A_MS3551061-300V2]; + my $path = q[/export/esa-sv-20201215-02/IL_seq_data/incoming/] . $rf_name; + my $test = Monitor::RunFolder->new( runfolder_path => $path, + id_run => 5222, + npg_tracking_schema => $schema, ); + isa_ok( $test, 'Monitor::RunFolder' ); + is( $test->run_folder(), $rf_name, 'run_folder value correct' ); isa_ok( $test->tracking_run(), 'npg_tracking::Schema::Result::Run', 'Object returned by tracking_run method' ); - is( $test->tracking_run()->current_run_status_description(), 'analysis pending', - 'Retrieve current run status' ); -} - -{ - my $mock_path = $MOCK_STAGING . '/IL4/incoming/101026_IL4_0095'; - my $test = Monitor::RunFolder->new( runfolder_path => $mock_path, - npg_tracking_schema => $schema, ); - - is( $test->tracking_run()->current_run_status_description(), 'run pending', - 'test is ready' ); + my $next_run_status = 'run in progress'; + ok( $test->tracking_run()->current_run_status_description() ne $next_run_status, + "current run status is different from '$next_run_status'" ); + throws_ok { $test->update_run_status() } + qr{Description should be provided}ms, + 'requires run status description argument'; + lives_ok { $test->update_run_status($next_run_status) } + 'can update run status run'; + is( $test->tracking_run()->current_run_status_description(), + $next_run_status, "run status updated to '$next_run_status'" ); throws_ok { $test->update_cycle_count() } qr{Latest cycle count not supplied}ms, 'requires latest cycle count argument'; - throws_ok { $test->update_run_status() } - qr{Description should be provided}ms, - 'requires run status description argument'; + my $current_cc = 120; + is( $test->tracking_run->actual_cycle_count(), $current_cc, + 'current actual cycle count'); + ok( !$test->update_cycle_count(5), + 'cycle count is not updated to a lower value' ); + is( $test->tracking_run->actual_cycle_count(), $current_cc, + 'current actual cycle count has not changed'); + ok( !$test->update_cycle_count($current_cc), + 'cycle count is not updated to the same value' ); + is( $test->tracking_run->actual_cycle_count(), $current_cc, + 'current actual cycle count has not changed'); + ok( $test->update_cycle_count(125), 'cycle count updated' ); + is( $test->tracking_run->actual_cycle_count(), 125, + 'cycle count updated correctly' ); +}; + +subtest 'test setting run tags' => sub { + plan tests => 5; - lives_ok { $test->update_run_status('run in progress') } - 'move run from \'pending\' to \'in progress\''; - is( $test->tracking_run()->current_run_status_description(), 'run in progress', - 'run status updated' ); - - is( $test->update_cycle_count(5), 1, 'cycle count updated' ); - is( $test->tracking_run->actual_cycle_count(), 5, 'cycle count updated correctly' ); - is( $test->update_cycle_count(5), 0, 'cycle count not updated' ); - is( $test->tracking_run->actual_cycle_count(), 5, 'cycle count has not changed' ); - - lives_ok { $test->update_run_status('run complete') } - 'move run from \'pending\' to \'in progress\''; - is( $test->tracking_run()->current_run_status_description(), 'run complete', - 'run status updated' ); - - is( $test->update_cycle_count(43), 1, 'cycle count updated'); - is( $test->tracking_run->actual_cycle_count(), 43, - 'cycle count updated' ); - is( $test->update_cycle_count(41), 0, 'cycle count not updated'); - is( $test->tracking_run->actual_cycle_count(), 43, - 'cycle count has not changed' ); -} - -{ my $basedir = tempdir( CLEANUP => 1 ); my $fs_run_folder = qq[$basedir/IL12/incoming/100721_IL12_05222]; make_path($fs_run_folder); - my $mock_path = $MOCK_STAGING . '/IL12/incoming/100721_IL12_05222'; my $fh; my $runinfofile = qq[$fs_run_folder/RunInfo.xml]; open($fh, '>', $runinfofile) or die "Could not open file '$runinfofile' $!"; @@ -105,12 +90,8 @@ ENDXML close $fh; my $test = Monitor::RunFolder->new( runfolder_path => $fs_run_folder, - npg_tracking_schema => $schema, ); - - move( "$mock_path/Data", "$mock_path/_Data" ) or die "Error $OS_ERROR"; + npg_tracking_schema => $schema ); lives_ok { $test->set_run_tags() } 'Call set_run_tags method without error'; - move( "$mock_path/_Data", "$mock_path/Data" ) or die "Error $OS_ERROR"; - is( $test->tracking_run()->is_tag_set('single_read'), 1, ' \'single_read\' tag is set on this run' ); is( $test->tracking_run()->is_tag_set('multiplex'), 0, @@ -119,8 +100,6 @@ ENDXML my $basedir2 = tempdir( CLEANUP => 1 ); my $fs_run_folder2 = qq[$basedir2/IL3/incoming/100622_IL3_01234]; make_path($fs_run_folder2); - my $mock_path2 = $MOCK_STAGING . '/IL3/incoming/100622_IL3_01234'; - system('cp', '-rp', $mock_path2, qq[$basedir2/IL3/incoming]); my $fh2; my $runinfofile2 = qq[$fs_run_folder2/RunInfo.xml]; open($fh2, '>', $runinfofile2) or die "Could not open file '$runinfofile2' $!"; @@ -151,14 +130,15 @@ ENDXML $test = Monitor::RunFolder->new( runfolder_path => $fs_run_folder2, npg_tracking_schema => $schema, ); $test->set_run_tags(); - is( $test->tracking_run()->is_tag_set('paired_read'), 1, ' \'paired_read\' tag is set on that run' ); is( $test->tracking_run()->is_tag_set('multiplex'), 1, ' \'multiplex\' tag is set on that run' ); -} +}; -{ +subtest 'test trimming lane count' => sub { + plan tests => 5; + my $run_info = q{ @@ -217,7 +197,7 @@ q{ $test->delete_superfluous_lanes(); is ($test->tracking_run()->run_lanes->count, 2, 'no change - run has two lanes'); -} +}; subtest 'workflow and instrument side - NovaSeq run' => sub { plan tests => 16; From ff1960db353d2d83f7d03b143e8814200289e018 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 30 Jan 2024 11:21:14 +0000 Subject: [PATCH 2/4] Deleted unused test runfolders for GA instriments. --- MANIFEST | 109 ------------------ t/data/gaii/ftp/Find_Me | 0 .../Data/Intensities/L001/.gitignore | 4 - .../Data/Intensities/L001/C1.1/.gitignore | 4 - .../Data/Intensities/L001/C10.1/.gitignore | 4 - .../Data/Intensities/L001/C11.1/.gitignore | 4 - .../Data/Intensities/L001/C12.1/.gitignore | 4 - .../Data/Intensities/L001/C13.1/.gitignore | 4 - .../Data/Intensities/L001/C14.1/.gitignore | 4 - .../Data/Intensities/L001/C15.1/.gitignore | 4 - .../Data/Intensities/L001/C16.1/.gitignore | 4 - .../Data/Intensities/L001/C17.1/.gitignore | 4 - .../Data/Intensities/L001/C18.1/.gitignore | 4 - .../Data/Intensities/L001/C19.1/.gitignore | 4 - .../Data/Intensities/L001/C2.1/.gitignore | 4 - .../Data/Intensities/L001/C20.1/.gitignore | 4 - .../Data/Intensities/L001/C21.1/.gitignore | 4 - .../Data/Intensities/L001/C22.1/.gitignore | 4 - 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index e69de29b..00000000 diff --git a/t/data/gaii/staging/IL12/incoming/100721_IL12_05222/Data/Intensities/L001/.gitignore b/t/data/gaii/staging/IL12/incoming/100721_IL12_05222/Data/Intensities/L001/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL12/incoming/100721_IL12_05222/Data/Intensities/L001/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C11.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C11.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C11.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C12.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C12.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C12.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C13.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C13.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C13.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C14.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C14.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C14.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C15.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C15.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C15.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C16.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C16.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C16.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C17.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C17.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C17.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C18.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C18.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C18.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C19.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C19.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C19.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C2.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C2.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C2.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C20.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C20.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C20.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C21.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C21.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C21.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C22.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C22.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C22.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C23.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C23.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C23.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C24.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C24.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C24.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C25.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C25.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C25.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C26.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C26.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C26.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C27.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C27.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C27.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C28.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C28.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C28.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C29.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C29.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C29.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C3.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C3.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C3.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C30.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C30.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C30.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C31.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C31.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C31.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C32.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C32.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C32.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C33.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C33.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C33.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C34.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C34.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C34.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C35.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C35.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C35.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C36.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C36.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C36.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C37.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C37.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C37.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C4.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C4.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C4.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C5.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C5.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C5.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C6.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C6.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C6.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C7.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C7.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C7.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C8.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C8.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C8.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C9.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C9.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C9.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L002/C1.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L002/C1.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L002/C1.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L002/C3.1/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L002/C3.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L002/C3.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L003/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L003/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L003/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L004/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L004/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L004/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L005/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L005/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L005/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L006/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L006/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L006/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L007/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L007/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L007/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L008/.gitignore b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L008/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L008/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/this_run_is_not_complete_yet b/t/data/gaii/staging/IL3/incoming/100622_IL3_01234/this_run_is_not_complete_yet deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/gaii/staging/IL3/skip_this_one/090810_IL12_3289/.gitignore b/t/data/gaii/staging/IL3/skip_this_one/090810_IL12_3289/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL3/skip_this_one/090810_IL12_3289/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL5/incoming/100708_IL3_04998/.gitignore b/t/data/gaii/staging/IL5/incoming/100708_IL3_04998/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL5/incoming/100708_IL3_04998/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL5/incoming/not_a_dir b/t/data/gaii/staging/IL5/incoming/not_a_dir deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/gaii/staging/IL5/incoming/not_a_valid_run_folder/.gitignore b/t/data/gaii/staging/IL5/incoming/not_a_valid_run_folder/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL5/incoming/not_a_valid_run_folder/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C11.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C11.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C11.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C12.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C12.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C12.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C13.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C13.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C13.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C14.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C14.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C14.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C15.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C15.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C15.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C16.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C16.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C16.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C17.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C17.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C17.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C18.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C18.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C18.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C19.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C19.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C19.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C2.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C2.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C2.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C20.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C20.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C20.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C21.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C21.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C21.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C22.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C22.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C22.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C23.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C23.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C23.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C24.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C24.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C24.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C25.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C25.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C25.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C26.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C26.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C26.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C27.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C27.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C27.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C28.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C28.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C28.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C29.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C29.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C29.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C3.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C3.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C3.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C30.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C30.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C30.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C31.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C31.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C31.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C32.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C32.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C32.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C33.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C33.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C33.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C34.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C34.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C34.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C35.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C35.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C35.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C36.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C36.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C36.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C37.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C37.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C37.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C38.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C38.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C38.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C39.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C39.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C39.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C4.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C4.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C4.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C40.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C40.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C40.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C41.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C41.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C41.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C42.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C42.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C42.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C43.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C43.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C43.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C44.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C44.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C44.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C45.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C45.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C45.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C46.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C46.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C46.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C47.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C47.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C47.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C48.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C48.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C48.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C49.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C49.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C49.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C5.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C5.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C5.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C50.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C50.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C50.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C51.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C51.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C51.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C52.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C52.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C52.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C53.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C53.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C53.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C54.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C54.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C54.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C6.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C6.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C6.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C7.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C7.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C7.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C8.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C8.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C8.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C9.1/.gitignore b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C9.1/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C9.1/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Recipe_GA2-PEM_2x76Cycle_v7.7.xml b/t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Recipe_GA2-PEM_2x76Cycle_v7.7.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/Data/reports/StatusUpdate.xml b/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/Data/reports/StatusUpdate.xml deleted file mode 100644 index fa09777c..00000000 --- a/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/Data/reports/StatusUpdate.xml +++ /dev/null @@ -1 +0,0 @@ -\ufeff1521521521511520 diff --git a/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RTAComplete.txt b/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RTAComplete.txt deleted file mode 100755 index f6d6b3e9..00000000 --- a/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RTAComplete.txt +++ /dev/null @@ -1 +0,0 @@ -Illumina RTA 1.7.45 diff --git a/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RunInfo.xml b/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RunInfo.xml deleted file mode 100755 index 2ee6f6b0..00000000 --- a/t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RunInfo.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - - SN292 - - - - - - - - - - - - - - - - - - \ No newline at end of file From 526c3eccdc576b336d928a454048d223157ee984 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 30 Jan 2024 16:02:16 +0000 Subject: [PATCH 3/4] Ensure none of the tests rely on parsing run folder name --- t/34-monitor-runfolder.t | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/t/34-monitor-runfolder.t b/t/34-monitor-runfolder.t index 4c1af76c..1179f986 100644 --- a/t/34-monitor-runfolder.t +++ b/t/34-monitor-runfolder.t @@ -62,7 +62,7 @@ subtest 'test setting run tags' => sub { plan tests => 5; my $basedir = tempdir( CLEANUP => 1 ); - my $fs_run_folder = qq[$basedir/IL12/incoming/100721_IL12_05222]; + my $fs_run_folder = qq[$basedir/IL_seq_data/incoming/run_folder_1]; make_path($fs_run_folder); my $fh; my $runinfofile = qq[$fs_run_folder/RunInfo.xml]; @@ -85,6 +85,7 @@ ENDXML print $fh <<"ENDXML"; + 1204 ENDXML close $fh; @@ -97,8 +98,7 @@ ENDXML is( $test->tracking_run()->is_tag_set('multiplex'), 0, ' \'multiplex\' tag is not set on this run' ); - my $basedir2 = tempdir( CLEANUP => 1 ); - my $fs_run_folder2 = qq[$basedir2/IL3/incoming/100622_IL3_01234]; + my $fs_run_folder2 = qq[$basedir/IL_seq_data/incoming/run_folder_2]; make_path($fs_run_folder2); my $fh2; my $runinfofile2 = qq[$fs_run_folder2/RunInfo.xml]; @@ -123,6 +123,7 @@ ENDXML print $fh2 <<"ENDXML"; + 4999 ENDXML close $fh2; @@ -161,40 +162,36 @@ q{ my $run_parameters = q{ + 1234 }; - my $root = tempdir( CLEANUP => 1 ); - my $rf = join q[/], $root, 'ILorHSany_sf50/incoming/150606_HS31_01234_B_HCYVGADXX'; + my $rf = join q[/], $root, 'IL_seq_data/incoming/run_folder1'; make_path $rf; - my $test = Monitor::RunFolder->new( runfolder_path => $rf, - npg_tracking_schema => $schema ); - foreach my $i ((1 .. 8)) { - $schema->resultset('RunLane')->create({ - id_run => 1234, position => $i, tile_count => 16, tracks => 2}); - - } - is ($test->tracking_run()->run_lanes->count, 8, 'run has eight lanes'); - - # create RunInfo file open my $fh, '>', join(q[/], $rf, 'RunInfo.xml'); print $fh $run_info; close $fh; - # create runParameters file open my $fh2, '>', join(q[/], $rf, 'runParameters.xml'); print $fh2 $run_parameters; close $fh2; + # Creade 8 lane records in the database + foreach my $i ((1 .. 8)) { + $schema->resultset('RunLane')->create({ + id_run => 1234, position => $i, tile_count => 16, tracks => 2}); + } + + my $test = Monitor::RunFolder->new( runfolder_path => $rf, + npg_tracking_schema => $schema ); + is ($test->tracking_run()->run_lanes->count, 8, 'run has eight lanes'); warnings_like { $test->delete_superfluous_lanes() } [ qr/Deleted lane 3/, qr/Deleted lane 4/, qr/Deleted lane 5/, qr/Deleted lane 6/, qr/Deleted lane 7/, qr/Deleted lane 8/], 'warnings about lane deletion'; - is ($test->lane_count, 2, 'two lanes listed in run info'); is ($test->tracking_run()->run_lanes->count, 2, 'now run has two lanes'); - $test->delete_superfluous_lanes(); is ($test->tracking_run()->run_lanes->count, 2, 'no change - run has two lanes'); }; From 0c5a1c4752b0615821d6b87a4f66e6c2b603dc49 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 8 Feb 2024 17:15:23 +0000 Subject: [PATCH 4/4] Implemented changes suggested by the reviewer --- t/34-monitor-runfolder-staging.t | 8 +++++--- t/34-monitor-runfolder.t | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/t/34-monitor-runfolder-staging.t b/t/34-monitor-runfolder-staging.t index 3723727d..3556492a 100644 --- a/t/34-monitor-runfolder-staging.t +++ b/t/34-monitor-runfolder-staging.t @@ -95,6 +95,8 @@ subtest 'computing glob and updating run data from filesystem' => sub { team => 'A', expected_cycle_count => 310, actual_cycle_count => 0, + folder_name => undef, + folder_path_glob => undef, }; my $run = $schema->resultset('Run')->find($id_run); $run->update($run_data); @@ -114,7 +116,7 @@ subtest 'computing glob and updating run data from filesystem' => sub { for my $dir (qw/incoming analysis outgoing/) { my $rfpath = $path; $rfpath =~ s/outgoing/$dir/; - note $rfpath; + note 'Testing ' . $rfpath; my $test = Monitor::RunFolder::Staging->new(runfolder_path => $rfpath); is($test->_get_folder_path_glob, $glob, "glob for /$dir/"); } @@ -155,7 +157,7 @@ subtest 'folder identifies copy complete for NovaSeq' => sub { for my $file_name (qw[CopyComplete Copycomplete copycomplete CopyComplete_old.txt ]) { - note $file_name; + note 'Testing ' . $file_name; my $path_to_wrong_copy_complete = qq[$fs_run_folder/$file_name]; touch_file($path_to_wrong_copy_complete); ok(!$run_folder->is_run_complete(), 'Run is not complete'); @@ -405,7 +407,7 @@ subtest 'monitoring size' => sub { ok( $size > 100, 'Find file size sum' ); }; -subtest 'seting file system permissions' => sub { +subtest 'setting file system permissions' => sub { plan tests => 4; my $tmpdir = tempdir( CLEANUP => 1 ); diff --git a/t/34-monitor-runfolder.t b/t/34-monitor-runfolder.t index 1179f986..4812332d 100644 --- a/t/34-monitor-runfolder.t +++ b/t/34-monitor-runfolder.t @@ -177,7 +177,7 @@ q{ print $fh2 $run_parameters; close $fh2; - # Creade 8 lane records in the database + # Create 8 lane records in the database foreach my $i ((1 .. 8)) { $schema->resultset('RunLane')->create({ id_run => 1234, position => $i, tile_count => 16, tracks => 2});